Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Sequencing and phylogenetic analysis

IS I Dewa Made Sukrama
JF Juliana Franciska
IS I Wayan Suardana
ask Ask a question
Favorite

The 16S rRNA gene of the strain 9 LAB isolate was sequenced using a genetic analyzer (ABI Prism 3130 and 3130×l Genetic Analyzer) at the 1st BASE DNA Sequencing, PT (Genetika Science, Jakarta). This procedure involved primers similar to those used for the PCR, and the outcomes were then manually edited to exclude the PCR primer binding sites, using MEGA version 5.2 software (The Pennsylvania State University) This modified result was automatically compared against the sequences of LAB available in databanks (www.ncbi.nlm.nih.gov) using the BLAST program on MEGA version 5.2 sofware. Therefore, the data obtained were subsequently used in phylogenetic tree construction by means of the neighbor-joining algorithm method [15,16].

Copyright and License information:  ©2020 Sukrama, .
Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A